General information for g4015.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as hypothetical.
Parent gene
- The parent gene g4015 is located on chr_3: 29529738..29530726 (- strand)
Gene structure
- The exon-intron structure of all isoforms are indicated below. CDS regions are colored in green. TSS and TTs that were predicted with CTR-Seq data are indicated in solid circle and squares, respectively. More specific data are shown in the table below.
| Chromosome | Gene | Transcript | Category | ID | Start | End |
|---|---|---|---|---|---|---|
| chr_3 | g4015 | g4015.t1 | TTS | g4015.t1 | 29528935 | 29528935 |
| chr_3 | g4015 | g4015.t1 | isoform | g4015.t1 | 29529738 | 29530726 |
| chr_3 | g4015 | g4015.t1 | exon | g4015.t1.exon1 | 29529738 | 29529889 |
| chr_3 | g4015 | g4015.t1 | cds | g4015.t1.CDS1 | 29529738 | 29529889 |
| chr_3 | g4015 | g4015.t1 | exon | g4015.t1.exon2 | 29529951 | 29530103 |
| chr_3 | g4015 | g4015.t1 | cds | g4015.t1.CDS2 | 29529951 | 29530103 |
| chr_3 | g4015 | g4015.t1 | exon | g4015.t1.exon3 | 29530486 | 29530726 |
| chr_3 | g4015 | g4015.t1 | cds | g4015.t1.CDS3 | 29530486 | 29530726 |
| chr_3 | g4015 | g4015.t1 | TSS | g4015.t1 | NA | NA |
Sequences
>g4015.t1 Gene=g4015 Length=546
ATGGCTTCCGCAAATAAATCGACGACGGATTTTTCAATTAATCATATTTTAAATCATGCC
GGTGAAAGATATAAAAAGTGTAAAATTAGTGCAAATTATGAAATGATAACATCATCAAGT
GATGAAGATTTAAGTGAAACTAGCAGTGAAAGAAGTGTTTATTTTGAAAATCAAAAATTT
ATTGAAATTCCAAATTTTAATTGGCTTAATTACACAAGATATAATATGCCTAGATTACCA
AGACCACAAAAAGGCCCATTAAAGAGAACATCAAGACTACCAAGAATTCCATTCACAACT
CATCAATTAAGTGAACTAGAGAAAGCGTATAAAACAGCAACCTATCTTAGCACAGAAGAT
GCAAATTTTCTCGCAAAACGACTTGAATTAACAAGTGTTCGTGTGAAAATTTGGTTCCAG
AACAGGAGGGCTCGCGATAGGCGTGATAGGCGTGAAAATAAAGATAATAATGACTCATTG
ACTAAAATATTAAATAATAGCAATGAGACTGATGAAGATAAAGAAGATGAAGTTATTATA
TCATGA
>g4015.t1 Gene=g4015 Length=181
MASANKSTTDFSINHILNHAGERYKKCKISANYEMITSSSDEDLSETSSERSVYFENQKF
IEIPNFNWLNYTRYNMPRLPRPQKGPLKRTSRLPRIPFTTHQLSELEKAYKTATYLSTED
ANFLAKRLELTSVRVKIWFQNRRARDRRDRRENKDNNDSLTKILNNSNETDEDKEDEVII
S
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 6 | g4015.t1 | CDD | cd00086 | homeodomain | 92 | 141 | 3.96427E-10 |
| 5 | g4015.t1 | Gene3D | G3DSA:1.10.10.60 | - | 78 | 165 | 3.3E-20 |
| 9 | g4015.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 145 | 181 | - |
| 2 | g4015.t1 | PANTHER | PTHR24333:SF5 | HOMEO BOX HB9 LIKE A-RELATED | 60 | 165 | 1.3E-20 |
| 3 | g4015.t1 | PANTHER | PTHR24333 | HOMEO BOX HB9 LIKE A-RELATED | 60 | 165 | 1.3E-20 |
| 1 | g4015.t1 | Pfam | PF00046 | Homeodomain | 94 | 148 | 4.8E-18 |
| 7 | g4015.t1 | ProSitePatterns | PS00027 | ‘Homeobox’ domain signature. | 124 | 147 | - |
| 10 | g4015.t1 | ProSiteProfiles | PS50071 | ‘Homeobox’ domain profile. | 89 | 149 | 17.475 |
| 8 | g4015.t1 | SMART | SM00389 | HOX_1 | 91 | 153 | 5.8E-17 |
| 4 | g4015.t1 | SUPERFAMILY | SSF46689 | Homeodomain-like | 86 | 151 | 2.69E-18 |
Transmembrane regions from TMHMM
Disordered region
IUPRED3 score over 0.5 is predictive of a disordered region.
GO terms from InterProScan
| GOID | TERM | ONTOLOGY |
|---|---|---|
| GO:0003677 | DNA binding | MF |
| GO:0000981 | DNA-binding transcription factor activity, RNA polymerase II-specific | MF |
| GO:0006355 | regulation of transcription, DNA-templated | BP |
KEGG
Orthology
- This transcript has been annotated with K09341 (homeobox protein MSX)
Pathway
- This transcript belongs to the following pathways
Expression
Transcript expression in Pv11 cells
TPM values are indicated as average +/- STDEV. 
Differential expression
Differentially expressed genes were identified with DESeq2 using the ‘run_DE_analysis.pl’ script from Trinity. Transcripts were determined as differentially expressed when (1) FDR < 0.05 (2) fold change > 2 (TPM calculated by RSEM). DE information and fold change between conditions are indicated in the plot below. There were no conditions that were differentially expressed